|
| Status |
Public on Feb 20, 2024 |
| Title |
Adult HSC ERCC1 Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HSC
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6 x 129S4S6/Sv F1
cell type: HSC
genotype: Ercc1-
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
total RNA was extracted using the RNeasy Mini Kit (QIAGEN)
RNA sequencing libraries were prepared using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® kit and NEBNext® Poly(A) mRNA Magnetic Isolation module kit following the manufacturer’s instructions. For hepatocytes, sequencing libraries were prepared using the NEBNext® UltraTM II RNA Library Prep Kit for Illumina® kit following the manufacturer’s instructions. Subsequently, all libraries were ligated to NEBNext® Multiplex Oligos for Illumina® (Dual Index Primer Set I)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads quality trimmed using trim_galore with q 30
Mapping to GRCm38 using hisat2
Differential expression analysis with cuffdiff
Gene set enrichment analysis with g:Profiler
Assembly: GRCm38 mouse genome
Supplementary files format and content: tab delimited cuffdiff output files of gene expression
|
| |
|
| Submission date |
Jun 23, 2022 |
| Last update date |
Feb 20, 2024 |
| Contact name |
Alastair Crisp |
| Organization name |
MRC Laboratory of Molecular Biology
|
| Street address |
Francis Crick Avenue
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0QH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE206778 |
Tissue-specific responses to DNA damage limit function and regulate ageing in progeroid mice |
|
| Relations |
| BioSample |
SAMN29264403 |
| SRA |
SRX15839566 |
